The certificates are now installed automagically for all the domains and subdomains you've got in your webhosting account (within 24 hours). You don't need to do anything at all. It gets auto renewed as well.

Installing Let's Encrypt SSL is now definitely easier than installing Cloudflare's Flexi SSL.. you don't need to do anything to have it installed... (of course, only for those on webhosts that enabled cPanel's AutoSSL feature):D :D :D